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Detailed information for vg0135017715:

Variant ID: vg0135017715 (JBrowse)	Variation Type: SNP
Chromosome: chr01	Position: 35017715
Reference Allele: C	Alternative Allele: G
Primary Allele: C	Secondary Allele: G

Inferred Ancestral Allele: Not determined.

Flanking Sequence (100 bp) in Reference Genome:

TTCGTCAGCACCCGCGGCAAGTGTTGTCAGCACCAGGTCGTCCAACTGTTGTCAGTTCTAGCAATGCACCTGGTATTGCTCCAATCTGGAGGCCCATCGA[C/G]
AAATCACCGCTCGGTAACCCCACGGGCAAGAAGATCCTACCCGTTACAGCTGACAAGACAGTTGCCCCTCCACCATCGAAGATCAACAAGCAGAGCAACG

Reverse complement sequence

CGTTGCTCTGCTTGTTGATCTTCGATGGTGGAGGGGCAACTGTCTTGTCAGCTGTAACGGGTAGGATCTTCTTGCCCGTGGGGTTACCGAGCGGTGATTT[G/C]
TCGATGGGCCTCCAGATTGGAGCAATACCAGGTGCATTGCTAGAACTGACAACAGTTGGACGACCTGGTGCTGACAACACTTGCCGCGGGTGCTGACGAA

Allele Frequencies:

Populations	Population Size	Frequency of C(primary allele)	Frequency of G(secondary allele)	Frequency of N	Frequency of DEL	Frequency of others Allele
All	4726	92.70%	4.30%	3.00%	0.00%	NA
All Indica	2759	95.10%	1.20%	3.62%	0.00%	NA
All Japonica	1512	99.60%	0.40%	0.00%	0.00%	NA
Aus	269	31.60%	55.40%	13.01%	0.00%	NA
Indica I	595	96.80%	0.50%	2.69%	0.00%	NA
Indica II	465	98.50%	0.60%	0.86%	0.00%	NA
Indica III	913	94.20%	0.90%	4.93%	0.00%	NA
Indica Intermediate	786	93.00%	2.50%	4.45%	0.00%	NA
Temperate Japonica	767	99.90%	0.10%	0.00%	0.00%	NA
Tropical Japonica	504	100.00%	0.00%	0.00%	0.00%	NA
Japonica Intermediate	241	97.90%	2.10%	0.00%	0.00%	NA
VI/Aromatic	96	83.30%	12.50%	4.17%	0.00%	NA
Intermediate	90	94.40%	2.20%	3.33%	0.00%	NA

Allele Effect:

Var ID	Var	Locus	snpEff Annotation	CooVar Annotation	Chromatin Accessibility Score	PolyPhen-2 Effect	PolyPhen-2 Score	SIFT Effect	SIFT Score
vg0135017715	C -> G	LOC_Os01g60560.1	missense_variant ; p.Asp460Glu; MODERATE	nonsynonymous_codon ; D460E	Average:40.008; most accessible tissue: Zhenshan97 flag leaf, score: 63.67	unknown	unknown	TOLERATED	0.09

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg0135017715	NA	4.32E-11	mr1499	All	YES	Genome-wide association analyses provide genetic and biochemical insights into natural variation in rice metabolism, Nat Genet, 46(7):714-21, PMID:24908251